Hydrogen pipeline network operation is important for balancing the hydrogen producing and consuming unit onsite. To make the operation efficient and stable, this article presents a mathematical program which incorporates equilibrium constraints (MPECs) for scheduling of hydrogen pipeline network between hydrogen producing and consuming units within a refinery. The developed model not only handles the multi-component and non-ideal nature of the hydrogen pipeline network, but also allows flow reversals and flow transitions inside the pipeline. A real refinery case study shows that the optimal schedule of pipeline storage could stabilize the hydrogen production, which improves the efficiency of the system. Operating safety is also ensured by the pressure constraints. (C) 2014 Elsevier Ltd. All rights reserved.